PLUMED 2: New feathers for an old bird

Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni

doi:10.1016/j.cpc.2013.09.018

Cited by 2,639 publications

(2,863 citation statements)

References 48 publications

(58 reference statements)

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“…21 Ideal A-form, fully stacked initial conformations were generated using the Make-NA web server (http://structure.usc.edu/make-na/server.html). The systems described in Table 1 were solvated in a truncated dodecahedral box with TIP3P 22 water molecules and neutralized by adding Na + counterions.…”

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confidence: 99%

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Bottaro

Banáš

Šponer

et al. 2016

J. Phys. Chem. Lett.

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179

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We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber\c{hi}OL3 force field. The estimated folding free energies are 30.2kJ/mol for UUCG and 7.5 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche+ region of {\alpha} and {\zeta} angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments.Comment: Journal of Physical Chemistry Letters (2016

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confidence: 99%

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Bottaro

Banáš

Šponer

et al. 2016

J. Phys. Chem. Lett.

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179

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“…(A) US QM/MM free energy profile for the κ torsion of a rCC dinucleotide indicating three main orientations ("conf1", "conf2", and "conf3"). The continuous line and error bars correspond to the average and standard deviation of the free energy, respectively, calculated from the energy profiles obtained after 20,21,22,23,24, and 25 ps of US simulation. A snapshot of the simulated system is shown, indicating in blue the QM region (rCC dinucleotide) and in green the MM region (water and K + ion).…”

Section: Puckering and C2'o2' Torsion Are Coupled Inmentioning

confidence: 99%

“…They include the following: (i) standard simulations in hairpin and kissing loop RNA motives ; (ii) potentials of mean force (PMF) of the  rotation at the dinucleotide (rCpC) level using umbrella sampling (US) with an 18° interval grid of the κ torsional space (500 ps equilibration and 2.5 ns of averaging per window); and (iii) Hamiltonian-replica exchange molecular dynamics (H-REMD) to evaluate the conformational landscape of two small RNA tetranucleotides (rGACC and rCCCC) for which experimental structural data in solution are available. 19,20 All calculations were performed using the parm99 force field 21,22 supplemented with the bsc0 23 and chiOL3 24,25 modifications for RNA; some control simulations were performed with a local experimental RNA version of the parmbsc1 forcefield. 26 Electroneutrality was achieved by adding K + and extra K + Cl -to generate a 150 mM concentration (taking Dang's parameters [27][28][29] to represent ions).…”

Section: Classical Simulationsmentioning

confidence: 99%

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

et al. 2016

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While DNA is mostly a primary carrier of genetic information and displays a regular duplex structure, RNA can form very complicated and conserved 3D structures displaying a large variety of functions, such as being an intermediary carrier of the genetic information, translating such information into the protein machinery of the cell, or even acting as a chemical catalyst. At the base of such functional diversity is the subtle balance between different backbone, nucleobase, and ribose conformations, finely regulated by the combination of hydrogen bonds and stacking interactions. Although an apparently simple chemical modification, the presence of the 2'OH in RNA has a profound effect in the ribonucleotide conformational balance, adding an extra layer of complexity to the interactions network in RNA. In the present work, we have combined database analysis with extensive molecular dynamics, quantum mechanics, and hybrid QM/MM simulations to provide direct evidence on the dramatic impact of the 2'OH conformation on sugar puckering. Calculations provide evidence that proteins can modulate the 2'OH conformation to drive sugar repuckering, leading then to the formation of bioactive conformations. In summary, the 2'OH group seems to be a primary molecular switch contributing to specific protein-RNA recognition.

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“…78,79 The PTMetaD-WTE calculations were performed and analyzed with the PLUMED2 plugin. 80 The PTMetaD-WTE simulations were performed for a total period of 180 ns/replica. The relative free-energy differences between all of the stable minima were monitored starting after 100 ns/replica and were unchanged after this point, so the simulation was terminated after an additional 80 ns/replica.…”

Section: Appendix C: Atomistic Simulation Detailsmentioning

confidence: 99%

Folding and insertion thermodynamics of the transmembrane WALP peptide

Bereau

Bennett

Pfaendtner

et al. 2015

The Journal of Chemical Physics

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A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions The Journal of Chemical Physics 146, 054501 (2017) The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA) n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum-in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence. C 2015 AIP Publishing LLC. [http://dx

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PLUMED 2: New feathers for an old bird

Cited by 2,639 publications

References 48 publications

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

Folding and insertion thermodynamics of the transmembrane WALP peptide

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